Multiple sequence alignment - TraesCS1B01G324100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1B01G324100 chr1B 100.000 2833 0 0 1 2833 549764757 549767589 0.000000e+00 5232
1 TraesCS1B01G324100 chr1B 96.581 1053 36 0 1 1053 480378223 480377171 0.000000e+00 1746
2 TraesCS1B01G324100 chr1B 96.496 1056 33 1 1 1052 549757894 549758949 0.000000e+00 1742
3 TraesCS1B01G324100 chr1B 89.679 1027 99 6 1129 2153 667761167 667762188 0.000000e+00 1303
4 TraesCS1B01G324100 chr1B 89.536 1013 100 5 1129 2140 74830521 74829514 0.000000e+00 1279
5 TraesCS1B01G324100 chr6B 96.604 1060 34 2 1 1058 417719001 417720060 0.000000e+00 1757
6 TraesCS1B01G324100 chr5B 96.768 1052 34 0 1 1052 337389114 337390165 0.000000e+00 1755
7 TraesCS1B01G324100 chr5B 96.679 1054 34 1 1 1053 305509471 305508418 0.000000e+00 1751
8 TraesCS1B01G324100 chr5B 96.578 1052 35 1 1 1052 307749633 307748583 0.000000e+00 1742
9 TraesCS1B01G324100 chr5B 96.486 1053 35 2 1 1052 445473833 445472782 0.000000e+00 1738
10 TraesCS1B01G324100 chr5B 91.575 1092 90 2 1053 2142 615957900 615956809 0.000000e+00 1506
11 TraesCS1B01G324100 chr5B 89.328 1012 97 9 1129 2140 257187608 257188608 0.000000e+00 1260
12 TraesCS1B01G324100 chr4B 96.496 1056 34 2 1 1053 179998559 179999614 0.000000e+00 1742
13 TraesCS1B01G324100 chr7B 96.486 1053 35 2 1 1053 215385576 215386626 0.000000e+00 1738
14 TraesCS1B01G324100 chr2A 88.799 1107 107 9 1044 2148 192131181 192130090 0.000000e+00 1341
15 TraesCS1B01G324100 chr1A 90.278 864 81 3 1279 2140 358923261 358924123 0.000000e+00 1127
16 TraesCS1B01G324100 chr1A 85.773 485 47 17 2216 2697 504572541 504573006 7.050000e-136 494
17 TraesCS1B01G324100 chr7A 85.500 1069 145 8 1055 2116 726905996 726904931 0.000000e+00 1107
18 TraesCS1B01G324100 chr7A 84.158 1111 162 12 1038 2138 586205685 586206791 0.000000e+00 1064
19 TraesCS1B01G324100 chr6A 85.009 1094 148 11 1055 2140 515061530 515060445 0.000000e+00 1098
20 TraesCS1B01G324100 chr1D 90.000 620 54 6 2216 2833 408464632 408465245 0.000000e+00 795


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G324100 chr1B 549764757 549767589 2832 False 5232 5232 100.000 1 2833 1 chr1B.!!$F2 2832
1 TraesCS1B01G324100 chr1B 480377171 480378223 1052 True 1746 1746 96.581 1 1053 1 chr1B.!!$R2 1052
2 TraesCS1B01G324100 chr1B 549757894 549758949 1055 False 1742 1742 96.496 1 1052 1 chr1B.!!$F1 1051
3 TraesCS1B01G324100 chr1B 667761167 667762188 1021 False 1303 1303 89.679 1129 2153 1 chr1B.!!$F3 1024
4 TraesCS1B01G324100 chr1B 74829514 74830521 1007 True 1279 1279 89.536 1129 2140 1 chr1B.!!$R1 1011
5 TraesCS1B01G324100 chr6B 417719001 417720060 1059 False 1757 1757 96.604 1 1058 1 chr6B.!!$F1 1057
6 TraesCS1B01G324100 chr5B 337389114 337390165 1051 False 1755 1755 96.768 1 1052 1 chr5B.!!$F2 1051
7 TraesCS1B01G324100 chr5B 305508418 305509471 1053 True 1751 1751 96.679 1 1053 1 chr5B.!!$R1 1052
8 TraesCS1B01G324100 chr5B 307748583 307749633 1050 True 1742 1742 96.578 1 1052 1 chr5B.!!$R2 1051
9 TraesCS1B01G324100 chr5B 445472782 445473833 1051 True 1738 1738 96.486 1 1052 1 chr5B.!!$R3 1051
10 TraesCS1B01G324100 chr5B 615956809 615957900 1091 True 1506 1506 91.575 1053 2142 1 chr5B.!!$R4 1089
11 TraesCS1B01G324100 chr5B 257187608 257188608 1000 False 1260 1260 89.328 1129 2140 1 chr5B.!!$F1 1011
12 TraesCS1B01G324100 chr4B 179998559 179999614 1055 False 1742 1742 96.496 1 1053 1 chr4B.!!$F1 1052
13 TraesCS1B01G324100 chr7B 215385576 215386626 1050 False 1738 1738 96.486 1 1053 1 chr7B.!!$F1 1052
14 TraesCS1B01G324100 chr2A 192130090 192131181 1091 True 1341 1341 88.799 1044 2148 1 chr2A.!!$R1 1104
15 TraesCS1B01G324100 chr1A 358923261 358924123 862 False 1127 1127 90.278 1279 2140 1 chr1A.!!$F1 861
16 TraesCS1B01G324100 chr7A 726904931 726905996 1065 True 1107 1107 85.500 1055 2116 1 chr7A.!!$R1 1061
17 TraesCS1B01G324100 chr7A 586205685 586206791 1106 False 1064 1064 84.158 1038 2138 1 chr7A.!!$F1 1100
18 TraesCS1B01G324100 chr6A 515060445 515061530 1085 True 1098 1098 85.009 1055 2140 1 chr6A.!!$R1 1085
19 TraesCS1B01G324100 chr1D 408464632 408465245 613 False 795 795 90.000 2216 2833 1 chr1D.!!$F1 617

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
837 846 0.464013 AGTCCGGAGATCGTCATCGT 60.464 55.0 3.06 0.0 38.33 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2312 2352 0.035439 GAATTTGGTCTCGCCCAGGA 60.035 55.0 0.0 0.0 35.49 3.86 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 5.142639 CCAATATGAACATCCAGGTTCCAT 58.857 41.667 1.87 0.00 45.12 3.41
378 379 1.918800 GCCGGGGAGTATATGGGCT 60.919 63.158 2.18 0.00 37.57 5.19
517 522 0.824759 CCCCTTCTCCTACTCCAACG 59.175 60.000 0.00 0.00 0.00 4.10
534 539 0.978146 ACGAGGGAGGTGGAATCCTG 60.978 60.000 0.00 0.00 38.02 3.86
535 540 0.978146 CGAGGGAGGTGGAATCCTGT 60.978 60.000 0.00 0.00 38.02 4.00
721 730 1.771565 TCCACCTCGGTCATATCGTT 58.228 50.000 0.00 0.00 35.57 3.85
775 784 2.011947 CATCATCATTGTCACCACGCT 58.988 47.619 0.00 0.00 0.00 5.07
837 846 0.464013 AGTCCGGAGATCGTCATCGT 60.464 55.000 3.06 0.00 38.33 3.73
924 933 0.523968 TACGACTACATCAACCGCGC 60.524 55.000 0.00 0.00 0.00 6.86
1077 1088 5.183140 GTCCTCCATAGCAAAGCAAGTTAAA 59.817 40.000 0.00 0.00 0.00 1.52
1096 1109 8.541899 AGTTAAAAAGAAGGGTAAACATCCAA 57.458 30.769 0.00 0.00 0.00 3.53
1098 1111 6.800072 AAAAAGAAGGGTAAACATCCAACA 57.200 33.333 0.00 0.00 0.00 3.33
1107 1120 7.892609 AGGGTAAACATCCAACACTAAATTTC 58.107 34.615 0.00 0.00 0.00 2.17
1120 1133 7.573968 ACACTAAATTTCAATCATAGGAGCC 57.426 36.000 0.00 0.00 0.00 4.70
1127 1140 5.607939 TTCAATCATAGGAGCCGAAGTAA 57.392 39.130 0.00 0.00 0.00 2.24
1167 1182 5.992217 GCTTCACCTAACTTTTTCTCTCTGA 59.008 40.000 0.00 0.00 0.00 3.27
1262 1283 0.813184 CAAGGCGACCAATGCTTGAT 59.187 50.000 0.00 0.00 0.00 2.57
1269 1291 3.002791 CGACCAATGCTTGATACAGTGT 58.997 45.455 0.00 0.00 31.44 3.55
1271 1293 2.489329 ACCAATGCTTGATACAGTGTGC 59.511 45.455 5.88 0.22 31.44 4.57
1276 1298 3.073678 TGCTTGATACAGTGTGCGAAAT 58.926 40.909 5.88 0.00 0.00 2.17
1317 1339 2.137523 GGTACACCTGTTGGTACGTTG 58.862 52.381 0.00 0.00 46.60 4.10
1337 1359 5.523552 CGTTGATGAAGGTATGATACAAGCA 59.476 40.000 4.83 0.00 0.00 3.91
1350 1372 9.875691 GTATGATACAAGCATCCATACTGATTA 57.124 33.333 0.00 0.00 0.00 1.75
1367 1389 0.037326 TTACTCTGCCACGCCAGAAG 60.037 55.000 3.18 1.40 41.02 2.85
1391 1413 5.719085 GGATAGCTTCAGAGAATCCTCCATA 59.281 44.000 0.00 0.00 40.30 2.74
1443 1465 3.773119 AGATGAAGCAATGGAAAAGGCAT 59.227 39.130 0.00 0.00 0.00 4.40
1449 1471 2.756760 GCAATGGAAAAGGCATCTCAGA 59.243 45.455 0.00 0.00 0.00 3.27
1468 1490 4.594491 TCAGATGGCCTTAGAATGCATCTA 59.406 41.667 3.32 0.52 39.71 1.98
1532 1560 4.665833 TCTTGAAGTCACGAAGGAAAGA 57.334 40.909 0.00 0.00 0.00 2.52
1640 1668 7.715657 AGTTTGCAAGACAGACAATGATTTTA 58.284 30.769 0.00 0.00 35.84 1.52
1641 1669 8.196771 AGTTTGCAAGACAGACAATGATTTTAA 58.803 29.630 0.00 0.00 35.84 1.52
1768 1797 2.029739 TCGGACGTATGCAAGAACTTGA 60.030 45.455 17.19 4.44 42.93 3.02
1778 1811 7.379529 CGTATGCAAGAACTTGAAAAATCACTT 59.620 33.333 17.19 0.00 42.93 3.16
1779 1812 9.034544 GTATGCAAGAACTTGAAAAATCACTTT 57.965 29.630 17.19 0.00 42.93 2.66
1976 2010 8.809066 ACTTTTAATTTGTACCTTTGTATCCCC 58.191 33.333 0.00 0.00 0.00 4.81
1995 2030 3.881688 CCCCACATTTGCAACATTTCAAA 59.118 39.130 0.00 0.00 36.72 2.69
2011 2046 5.398603 TTTCAAAATATTCATGTGCCCGT 57.601 34.783 0.00 0.00 0.00 5.28
2031 2071 8.426489 TGCCCGTTTTGTTTACTATCTCTATAT 58.574 33.333 0.00 0.00 0.00 0.86
2070 2110 1.537202 GACCATGCACTGTTCCACTTC 59.463 52.381 0.00 0.00 0.00 3.01
2073 2113 3.009473 ACCATGCACTGTTCCACTTCTAT 59.991 43.478 0.00 0.00 0.00 1.98
2082 2122 7.386299 GCACTGTTCCACTTCTATATCAATAGG 59.614 40.741 0.00 0.00 36.49 2.57
2142 2182 0.743345 GCACGGGTTAGGCTAGTTGG 60.743 60.000 0.00 0.00 0.00 3.77
2148 2188 3.387050 CGGGTTAGGCTAGTTGGTTCTAT 59.613 47.826 0.00 0.00 0.00 1.98
2149 2189 4.704965 GGGTTAGGCTAGTTGGTTCTATG 58.295 47.826 0.00 0.00 0.00 2.23
2151 2191 4.127907 GTTAGGCTAGTTGGTTCTATGGC 58.872 47.826 0.00 0.00 0.00 4.40
2152 2192 2.196595 AGGCTAGTTGGTTCTATGGCA 58.803 47.619 0.00 0.00 0.00 4.92
2154 2194 3.010138 AGGCTAGTTGGTTCTATGGCAAA 59.990 43.478 0.00 0.00 0.00 3.68
2155 2195 3.378427 GGCTAGTTGGTTCTATGGCAAAG 59.622 47.826 0.00 0.00 0.00 2.77
2156 2196 4.010349 GCTAGTTGGTTCTATGGCAAAGT 58.990 43.478 0.00 0.00 0.00 2.66
2157 2197 4.095036 GCTAGTTGGTTCTATGGCAAAGTC 59.905 45.833 0.00 0.00 0.00 3.01
2158 2198 4.373156 AGTTGGTTCTATGGCAAAGTCT 57.627 40.909 0.00 0.00 0.00 3.24
2159 2199 5.499004 AGTTGGTTCTATGGCAAAGTCTA 57.501 39.130 0.00 0.00 0.00 2.59
2160 2200 6.067217 AGTTGGTTCTATGGCAAAGTCTAT 57.933 37.500 0.00 0.00 0.00 1.98
2161 2201 6.116126 AGTTGGTTCTATGGCAAAGTCTATC 58.884 40.000 0.00 0.00 0.00 2.08
2162 2202 4.693283 TGGTTCTATGGCAAAGTCTATCG 58.307 43.478 0.00 0.00 0.00 2.92
2163 2203 4.404394 TGGTTCTATGGCAAAGTCTATCGA 59.596 41.667 0.00 0.00 0.00 3.59
2164 2204 4.985409 GGTTCTATGGCAAAGTCTATCGAG 59.015 45.833 0.00 0.00 0.00 4.04
2165 2205 4.244425 TCTATGGCAAAGTCTATCGAGC 57.756 45.455 0.00 0.00 0.00 5.03
2166 2206 1.858091 ATGGCAAAGTCTATCGAGCG 58.142 50.000 0.00 0.00 0.00 5.03
2167 2207 0.806102 TGGCAAAGTCTATCGAGCGC 60.806 55.000 0.00 0.00 0.00 5.92
2168 2208 1.491505 GGCAAAGTCTATCGAGCGCC 61.492 60.000 2.29 0.00 0.00 6.53
2169 2209 0.806102 GCAAAGTCTATCGAGCGCCA 60.806 55.000 2.29 0.00 0.00 5.69
2170 2210 1.640428 CAAAGTCTATCGAGCGCCAA 58.360 50.000 2.29 0.00 0.00 4.52
2171 2211 1.324736 CAAAGTCTATCGAGCGCCAAC 59.675 52.381 2.29 0.00 0.00 3.77
2172 2212 0.818296 AAGTCTATCGAGCGCCAACT 59.182 50.000 2.29 0.00 0.00 3.16
2173 2213 1.676746 AGTCTATCGAGCGCCAACTA 58.323 50.000 2.29 0.00 0.00 2.24
2174 2214 2.022195 AGTCTATCGAGCGCCAACTAA 58.978 47.619 2.29 0.00 0.00 2.24
2175 2215 2.033550 AGTCTATCGAGCGCCAACTAAG 59.966 50.000 2.29 0.00 0.00 2.18
2176 2216 1.132588 CTATCGAGCGCCAACTAAGC 58.867 55.000 2.29 0.00 0.00 3.09
2177 2217 0.744874 TATCGAGCGCCAACTAAGCT 59.255 50.000 2.29 0.00 44.80 3.74
2178 2218 0.744874 ATCGAGCGCCAACTAAGCTA 59.255 50.000 2.29 0.00 41.84 3.32
2179 2219 0.528924 TCGAGCGCCAACTAAGCTAA 59.471 50.000 2.29 0.00 41.84 3.09
2180 2220 0.924090 CGAGCGCCAACTAAGCTAAG 59.076 55.000 2.29 0.00 41.84 2.18
2181 2221 1.469251 CGAGCGCCAACTAAGCTAAGA 60.469 52.381 2.29 0.00 41.84 2.10
2182 2222 2.197577 GAGCGCCAACTAAGCTAAGAG 58.802 52.381 2.29 0.00 41.84 2.85
2183 2223 1.134670 AGCGCCAACTAAGCTAAGAGG 60.135 52.381 2.29 0.00 39.74 3.69
2184 2224 1.291132 CGCCAACTAAGCTAAGAGGC 58.709 55.000 6.96 6.96 37.63 4.70
2185 2225 1.291132 GCCAACTAAGCTAAGAGGCG 58.709 55.000 0.00 0.00 37.29 5.52
2186 2226 1.291132 CCAACTAAGCTAAGAGGCGC 58.709 55.000 0.00 0.00 37.29 6.53
2187 2227 1.134670 CCAACTAAGCTAAGAGGCGCT 60.135 52.381 7.64 0.00 38.30 5.92
2188 2228 1.929836 CAACTAAGCTAAGAGGCGCTG 59.070 52.381 7.64 0.00 36.45 5.18
2189 2229 1.475403 ACTAAGCTAAGAGGCGCTGA 58.525 50.000 7.64 0.00 36.45 4.26
2190 2230 1.407258 ACTAAGCTAAGAGGCGCTGAG 59.593 52.381 7.64 0.00 40.03 3.35
2191 2231 0.747255 TAAGCTAAGAGGCGCTGAGG 59.253 55.000 7.64 0.00 36.45 3.86
2192 2232 1.965754 AAGCTAAGAGGCGCTGAGGG 61.966 60.000 7.64 0.00 36.45 4.30
2193 2233 2.107953 CTAAGAGGCGCTGAGGGC 59.892 66.667 13.60 13.60 40.84 5.19
2203 2243 4.514577 CTGAGGGCGCCGTAGTGG 62.515 72.222 23.69 8.56 42.50 4.00
2205 2245 4.208686 GAGGGCGCCGTAGTGGAG 62.209 72.222 23.69 0.00 42.00 3.86
2210 2250 2.202623 CGCCGTAGTGGAGCACTC 60.203 66.667 0.00 0.00 41.21 3.51
2211 2251 2.184579 GCCGTAGTGGAGCACTCC 59.815 66.667 9.88 9.88 41.21 3.85
2246 2286 0.677842 ACCGTGGTGTTAGTCAGTCC 59.322 55.000 0.00 0.00 0.00 3.85
2289 2329 1.139853 CAGCCTAGTGATTCCCCTGAC 59.860 57.143 0.00 0.00 0.00 3.51
2293 2333 1.137086 CTAGTGATTCCCCTGACGTGG 59.863 57.143 0.00 0.00 0.00 4.94
2298 2338 0.544357 ATTCCCCTGACGTGGACTCA 60.544 55.000 0.00 0.00 0.00 3.41
2305 2345 3.628280 GACGTGGACTCAGGCCGTC 62.628 68.421 0.00 0.00 40.71 4.79
2310 2350 2.128507 GGACTCAGGCCGTCTAGGG 61.129 68.421 8.87 0.00 41.48 3.53
2320 2360 3.541713 GTCTAGGGCTCCTGGGCG 61.542 72.222 4.16 0.00 41.87 6.13
2321 2361 3.751018 TCTAGGGCTCCTGGGCGA 61.751 66.667 4.16 0.00 41.87 5.54
2323 2363 3.740495 CTAGGGCTCCTGGGCGAGA 62.740 68.421 0.00 0.00 41.87 4.04
2329 2369 1.604378 CTCCTGGGCGAGACCAAAT 59.396 57.895 0.00 0.00 40.68 2.32
2351 2391 1.823169 TTGTCACGAGCCTACCCCAC 61.823 60.000 0.00 0.00 0.00 4.61
2487 2527 7.918643 AGTGTTACCAAATTTCAAAAAGCATG 58.081 30.769 0.00 0.00 0.00 4.06
2490 2530 5.172460 ACCAAATTTCAAAAAGCATGCAC 57.828 34.783 21.98 0.00 0.00 4.57
2552 2592 8.366401 TCATGACTATTTTCTTGCCAAATTTGA 58.634 29.630 19.86 0.00 0.00 2.69
2605 2645 7.859875 CGAAATTGCAAAATGTTACCCAATTTT 59.140 29.630 1.71 0.00 40.73 1.82
2664 2705 1.244816 GAAGAAGAAAACCGGTGGGG 58.755 55.000 8.52 0.00 43.62 4.96
2674 2715 2.113139 CGGTGGGGACAAAGCAGT 59.887 61.111 0.00 0.00 46.06 4.40
2715 2756 2.353189 CCCATTACCGTGGTGGCA 59.647 61.111 0.72 0.00 43.94 4.92
2730 2771 1.729131 GGCAATGCACGTTTGGTCG 60.729 57.895 7.79 0.00 0.00 4.79
2733 2774 0.317770 CAATGCACGTTTGGTCGCTT 60.318 50.000 0.00 0.00 0.00 4.68
2743 2784 1.844544 TTGGTCGCTTCCCCTAACCC 61.845 60.000 0.00 0.00 0.00 4.11
2759 2800 2.754946 ACCCGTTCTCGCAATAGAAA 57.245 45.000 0.00 0.00 37.24 2.52
2764 2805 4.332819 CCCGTTCTCGCAATAGAAATTTCT 59.667 41.667 23.53 23.53 37.24 2.52
2796 2837 2.335681 TGAATAGGGACTGTGGTGGA 57.664 50.000 0.00 0.00 41.52 4.02
2798 2839 2.225522 TGAATAGGGACTGTGGTGGAGA 60.226 50.000 0.00 0.00 41.52 3.71
2806 2847 1.204941 ACTGTGGTGGAGATTCTACGC 59.795 52.381 0.43 0.43 0.00 4.42
2809 2850 0.681887 TGGTGGAGATTCTACGCGGA 60.682 55.000 12.47 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 1.084289 GAAACCTTAAGCGTGCGGAT 58.916 50.000 0.00 0.00 0.00 4.18
253 254 3.002042 TCGATCTTTACGTCTCGACCATC 59.998 47.826 0.00 0.00 35.41 3.51
333 334 1.407989 CCGTAACTCTCCGGTACTCCT 60.408 57.143 0.00 0.00 39.38 3.69
378 379 2.011122 TTCCCGTTTGGCCCAATAAA 57.989 45.000 0.00 0.00 0.00 1.40
390 391 2.952116 CCTCTCTCCTCTATTCCCGTT 58.048 52.381 0.00 0.00 0.00 4.44
517 522 1.290134 AACAGGATTCCACCTCCCTC 58.710 55.000 5.29 0.00 38.32 4.30
721 730 1.740296 GCTTCGCCTAAACTCCGCA 60.740 57.895 0.00 0.00 0.00 5.69
743 752 1.364171 GATGATGCTCTACCGGCGT 59.636 57.895 6.01 0.00 0.00 5.68
825 834 1.914634 GTTCAGCACGATGACGATCT 58.085 50.000 0.00 0.00 42.66 2.75
837 846 0.461870 AGTTCAGCACACGTTCAGCA 60.462 50.000 6.43 0.00 0.00 4.41
970 979 1.038130 TAGCAACGAGAGGGGAGAGC 61.038 60.000 0.00 0.00 0.00 4.09
1041 1050 1.131303 TGGAGGACGTGTTGGGGAAT 61.131 55.000 0.00 0.00 0.00 3.01
1077 1088 5.454966 AGTGTTGGATGTTTACCCTTCTTT 58.545 37.500 0.00 0.00 0.00 2.52
1096 1109 6.260936 CGGCTCCTATGATTGAAATTTAGTGT 59.739 38.462 0.00 0.00 0.00 3.55
1098 1111 6.591935 TCGGCTCCTATGATTGAAATTTAGT 58.408 36.000 0.00 0.00 0.00 2.24
1107 1120 4.950050 AGTTACTTCGGCTCCTATGATTG 58.050 43.478 0.00 0.00 0.00 2.67
1120 1133 3.761311 AGAGCTTACCGAGTTACTTCG 57.239 47.619 0.00 0.00 40.18 3.79
1262 1283 5.242434 AGACCAATTATTTCGCACACTGTA 58.758 37.500 0.00 0.00 0.00 2.74
1269 1291 8.325421 TGTACTTTTAGACCAATTATTTCGCA 57.675 30.769 0.00 0.00 0.00 5.10
1271 1293 9.769093 CCTTGTACTTTTAGACCAATTATTTCG 57.231 33.333 0.00 0.00 0.00 3.46
1276 1298 8.658619 TGTACCCTTGTACTTTTAGACCAATTA 58.341 33.333 4.68 0.00 46.19 1.40
1317 1339 6.233434 TGGATGCTTGTATCATACCTTCATC 58.767 40.000 9.86 9.86 0.00 2.92
1337 1359 4.262207 CGTGGCAGAGTAATCAGTATGGAT 60.262 45.833 0.00 0.00 36.16 3.41
1350 1372 2.345244 CTTCTGGCGTGGCAGAGT 59.655 61.111 22.81 0.00 0.00 3.24
1367 1389 3.900601 TGGAGGATTCTCTGAAGCTATCC 59.099 47.826 0.00 1.75 39.86 2.59
1391 1413 2.776536 AGCTGCCTCTCCTTCATATGTT 59.223 45.455 1.90 0.00 0.00 2.71
1443 1465 2.773661 TGCATTCTAAGGCCATCTGAGA 59.226 45.455 5.01 0.00 34.24 3.27
1510 1538 5.018539 TCTTTCCTTCGTGACTTCAAGAA 57.981 39.130 7.28 7.28 40.91 2.52
1523 1551 6.970484 TCTTGCTGTAAACAATCTTTCCTTC 58.030 36.000 0.00 0.00 0.00 3.46
1532 1560 4.457257 GCCTTCTCTCTTGCTGTAAACAAT 59.543 41.667 0.00 0.00 0.00 2.71
1610 1638 2.607635 TGTCTGTCTTGCAAACTCGTTC 59.392 45.455 0.00 0.00 0.00 3.95
1640 1668 5.927281 AGAAGCCATTGCATATCTTTGTT 57.073 34.783 0.00 0.00 41.13 2.83
1641 1669 5.927281 AAGAAGCCATTGCATATCTTTGT 57.073 34.783 0.00 0.00 41.13 2.83
1778 1811 7.255660 GGATTGGTGCCCGTAATAAAATGATAA 60.256 37.037 0.00 0.00 0.00 1.75
1779 1812 6.207810 GGATTGGTGCCCGTAATAAAATGATA 59.792 38.462 0.00 0.00 0.00 2.15
1790 1823 2.270850 GCAGGATTGGTGCCCGTA 59.729 61.111 0.00 0.00 34.67 4.02
1793 1826 2.757099 CCTGCAGGATTGGTGCCC 60.757 66.667 29.88 0.00 40.43 5.36
1822 1855 6.737720 AGTTGCTAGTGGATTAGATCATCA 57.262 37.500 0.00 0.00 0.00 3.07
1888 1921 1.661112 GTTCGCTGCAGACATAGAACC 59.339 52.381 20.43 5.76 36.70 3.62
1976 2010 9.880064 TGAATATTTTGAAATGTTGCAAATGTG 57.120 25.926 0.00 0.00 34.36 3.21
1995 2030 4.799564 ACAAAACGGGCACATGAATATT 57.200 36.364 0.00 0.00 0.00 1.28
2004 2039 4.694037 AGAGATAGTAAACAAAACGGGCAC 59.306 41.667 0.00 0.00 0.00 5.01
2052 2092 1.901591 AGAAGTGGAACAGTGCATGG 58.098 50.000 0.00 0.00 43.84 3.66
2120 2160 0.903454 ACTAGCCTAACCCGTGCAGT 60.903 55.000 0.00 0.00 0.00 4.40
2122 2162 0.036765 CAACTAGCCTAACCCGTGCA 60.037 55.000 0.00 0.00 0.00 4.57
2125 2165 1.277273 GAACCAACTAGCCTAACCCGT 59.723 52.381 0.00 0.00 0.00 5.28
2142 2182 4.446051 GCTCGATAGACTTTGCCATAGAAC 59.554 45.833 0.00 0.00 42.67 3.01
2148 2188 0.806102 GCGCTCGATAGACTTTGCCA 60.806 55.000 0.00 0.00 42.67 4.92
2149 2189 1.491505 GGCGCTCGATAGACTTTGCC 61.492 60.000 7.64 0.00 42.67 4.52
2151 2191 1.324736 GTTGGCGCTCGATAGACTTTG 59.675 52.381 7.64 0.00 42.67 2.77
2152 2192 1.204941 AGTTGGCGCTCGATAGACTTT 59.795 47.619 7.64 0.00 42.67 2.66
2154 2194 1.676746 TAGTTGGCGCTCGATAGACT 58.323 50.000 7.64 3.90 42.67 3.24
2155 2195 2.386249 CTTAGTTGGCGCTCGATAGAC 58.614 52.381 7.64 0.00 42.67 2.59
2156 2196 3.587113 AGCTTAGTTGGCGCTCGATAGA 61.587 50.000 7.64 0.00 38.01 1.98
2157 2197 1.132588 GCTTAGTTGGCGCTCGATAG 58.867 55.000 7.64 0.00 0.00 2.08
2158 2198 0.744874 AGCTTAGTTGGCGCTCGATA 59.255 50.000 7.64 0.00 34.52 2.92
2159 2199 0.744874 TAGCTTAGTTGGCGCTCGAT 59.255 50.000 7.64 0.00 35.33 3.59
2160 2200 0.528924 TTAGCTTAGTTGGCGCTCGA 59.471 50.000 7.64 0.00 35.33 4.04
2161 2201 0.924090 CTTAGCTTAGTTGGCGCTCG 59.076 55.000 7.64 0.00 35.33 5.03
2162 2202 2.197577 CTCTTAGCTTAGTTGGCGCTC 58.802 52.381 7.64 0.00 35.33 5.03
2163 2203 1.134670 CCTCTTAGCTTAGTTGGCGCT 60.135 52.381 7.64 0.00 37.77 5.92
2164 2204 1.291132 CCTCTTAGCTTAGTTGGCGC 58.709 55.000 0.00 0.00 34.52 6.53
2165 2205 1.291132 GCCTCTTAGCTTAGTTGGCG 58.709 55.000 18.10 0.00 34.52 5.69
2166 2206 1.291132 CGCCTCTTAGCTTAGTTGGC 58.709 55.000 20.94 20.94 34.77 4.52
2167 2207 1.134670 AGCGCCTCTTAGCTTAGTTGG 60.135 52.381 2.29 0.52 41.52 3.77
2168 2208 1.929836 CAGCGCCTCTTAGCTTAGTTG 59.070 52.381 2.29 0.00 42.52 3.16
2169 2209 1.825474 TCAGCGCCTCTTAGCTTAGTT 59.175 47.619 2.29 0.00 42.52 2.24
2170 2210 1.407258 CTCAGCGCCTCTTAGCTTAGT 59.593 52.381 2.29 0.00 42.52 2.24
2171 2211 1.269517 CCTCAGCGCCTCTTAGCTTAG 60.270 57.143 2.29 0.00 42.52 2.18
2172 2212 0.747255 CCTCAGCGCCTCTTAGCTTA 59.253 55.000 2.29 0.00 42.52 3.09
2173 2213 1.519719 CCTCAGCGCCTCTTAGCTT 59.480 57.895 2.29 0.00 42.52 3.74
2174 2214 2.430610 CCCTCAGCGCCTCTTAGCT 61.431 63.158 2.29 0.00 45.74 3.32
2175 2215 2.107953 CCCTCAGCGCCTCTTAGC 59.892 66.667 2.29 0.00 0.00 3.09
2176 2216 2.107953 GCCCTCAGCGCCTCTTAG 59.892 66.667 2.29 0.00 0.00 2.18
2186 2226 4.514577 CCACTACGGCGCCCTCAG 62.515 72.222 23.46 17.55 0.00 3.35
2188 2228 4.208686 CTCCACTACGGCGCCCTC 62.209 72.222 23.46 0.00 33.14 4.30
2192 2232 4.436998 AGTGCTCCACTACGGCGC 62.437 66.667 6.90 0.00 43.46 6.53
2193 2233 2.202623 GAGTGCTCCACTACGGCG 60.203 66.667 4.80 4.80 45.44 6.46
2194 2234 2.184579 GGAGTGCTCCACTACGGC 59.815 66.667 13.00 0.00 45.44 5.68
2203 2243 2.490115 CCATCCGACTATAGGAGTGCTC 59.510 54.545 4.43 0.00 41.66 4.26
2204 2244 2.108425 TCCATCCGACTATAGGAGTGCT 59.892 50.000 4.43 0.00 41.66 4.40
2205 2245 2.229302 GTCCATCCGACTATAGGAGTGC 59.771 54.545 4.43 0.00 41.66 4.40
2206 2246 3.253677 GTGTCCATCCGACTATAGGAGTG 59.746 52.174 4.43 0.00 42.49 3.51
2207 2247 3.488363 GTGTCCATCCGACTATAGGAGT 58.512 50.000 4.43 0.00 42.49 3.85
2208 2248 2.820787 GGTGTCCATCCGACTATAGGAG 59.179 54.545 4.43 0.00 42.49 3.69
2209 2249 2.872732 GGTGTCCATCCGACTATAGGA 58.127 52.381 4.43 0.00 42.49 2.94
2246 2286 0.101759 CAGCATCCCAAAGCAATCCG 59.898 55.000 0.00 0.00 0.00 4.18
2289 2329 1.994507 CTAGACGGCCTGAGTCCACG 61.995 65.000 0.00 0.00 39.31 4.94
2293 2333 2.787567 GCCCTAGACGGCCTGAGTC 61.788 68.421 0.00 0.24 43.66 3.36
2305 2345 3.230245 CTCGCCCAGGAGCCCTAG 61.230 72.222 0.00 0.00 29.64 3.02
2310 2350 2.543067 ATTTGGTCTCGCCCAGGAGC 62.543 60.000 0.00 0.00 35.49 4.70
2312 2352 0.035439 GAATTTGGTCTCGCCCAGGA 60.035 55.000 0.00 0.00 35.49 3.86
2320 2360 3.120511 GCTCGTGACAAGAATTTGGTCTC 60.121 47.826 0.00 0.00 38.66 3.36
2321 2361 2.808543 GCTCGTGACAAGAATTTGGTCT 59.191 45.455 0.00 0.00 38.66 3.85
2323 2363 1.880027 GGCTCGTGACAAGAATTTGGT 59.120 47.619 0.00 0.00 38.66 3.67
2329 2369 0.606604 GGGTAGGCTCGTGACAAGAA 59.393 55.000 0.00 0.00 0.00 2.52
2359 2399 1.714794 AGATTCTCAAACTGACGGCG 58.285 50.000 4.80 4.80 0.00 6.46
2360 2400 4.691216 ACTTTAGATTCTCAAACTGACGGC 59.309 41.667 0.00 0.00 0.00 5.68
2468 2508 4.639310 TGTGCATGCTTTTTGAAATTTGGT 59.361 33.333 20.33 0.00 0.00 3.67
2487 2527 7.859598 TCATGAACACCATTTAAAATTTGTGC 58.140 30.769 0.00 0.00 31.94 4.57
2572 2612 9.871299 GGTAACATTTTGCAATTTCGTAAAAAT 57.129 25.926 0.00 0.00 34.76 1.82
2577 2617 6.085555 TGGGTAACATTTTGCAATTTCGTA 57.914 33.333 0.00 0.00 39.74 3.43
2578 2618 4.950050 TGGGTAACATTTTGCAATTTCGT 58.050 34.783 0.00 0.00 39.74 3.85
2579 2619 5.914085 TTGGGTAACATTTTGCAATTTCG 57.086 34.783 0.00 0.00 39.74 3.46
2638 2679 5.243060 CCACCGGTTTTCTTCTTCCTTTTAT 59.757 40.000 2.97 0.00 0.00 1.40
2651 2692 0.671796 CTTTGTCCCCACCGGTTTTC 59.328 55.000 2.97 0.00 0.00 2.29
2664 2705 3.255642 TGGGCTTTCAATACTGCTTTGTC 59.744 43.478 0.00 0.00 0.00 3.18
2708 2749 1.067084 CAAACGTGCATTGCCACCA 59.933 52.632 6.12 0.00 32.10 4.17
2709 2750 1.664333 CCAAACGTGCATTGCCACC 60.664 57.895 6.12 0.00 32.10 4.61
2710 2751 0.939106 GACCAAACGTGCATTGCCAC 60.939 55.000 6.12 3.87 0.00 5.01
2715 2756 0.040425 GAAGCGACCAAACGTGCATT 60.040 50.000 0.00 0.00 35.59 3.56
2730 2771 0.107800 GAGAACGGGTTAGGGGAAGC 60.108 60.000 0.00 0.00 34.62 3.86
2733 2774 2.353610 GCGAGAACGGGTTAGGGGA 61.354 63.158 0.00 0.00 40.15 4.81
2743 2784 6.766084 AGAAGAAATTTCTATTGCGAGAACG 58.234 36.000 20.76 0.00 36.28 3.95
2764 2805 8.390921 ACAGTCCCTATTCATTAAGGAAAAGAA 58.609 33.333 6.65 0.00 34.58 2.52
2796 2837 1.814527 GGGTGTCCGCGTAGAATCT 59.185 57.895 4.92 0.00 0.00 2.40
2809 2850 4.493547 CAACATTTTTATGCATCGGGTGT 58.506 39.130 0.19 0.41 0.00 4.16


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.